In June 2005 Citrx released a document outlining the migration to Presentation Server 4.0. This document covers the recommended path to migrate to PS4.0.

Some Key Points:

Citrix only supports upgrading from FR3 and PS3.0. Directly upgrading from earlier versions such as FR1 and FR2 are not supported.

Upgrading operating systems from 2000 to 2003, Citrix recommends performing a clean install of 2003 Server and Presentation Server 4.0.

In this migration document, Citrix recommends only maintaining a farm containing mixed versions of Presentation Server for a short time.

From my experence with a mixed Farm, FR3 and PS4.0. Once you modify an appication object with the PS4.0 Management Console that object is no longer managable with the FR3 Management Console.

The Citrix Presentation Server 4 Migration Guide PDF